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PubMed2006

Polyphyly and gene flow between non-sibling Heliconius species.

BACKGROUND: The view that gene flow between related animal species is rare and evolutionarily unimportant largely antedates sensitive molecular techniques. Here we use DNA sequencing to investigate a pair of morphologically and ecologically divergent, non-sibling butterfly species, Heliconius cydno and H. melpomene (Lepidoptera: Nymphalidae), whose distributions overlap in Central and Northwestern South America. RESULTS: In these taxa, we sequenced 30-45 haplotypes per locus of a mitochondrial region containing the genes for cytochrome oxidase subunits I and II (CoI/CoII), and intron-spanning fragments of three unlinked nuclear loci: triose-phosphate isomerase (Tpi), mannose-6-phosphate isomerase (Mpi) and cubitus interruptus (Ci) genes. A fifth gene, dopa decarboxylase (Ddc) produced sequence data likely to be from different duplicate loci in some of the taxa, and so was excluded. Mitochondrial and Tpi genealogies are consistent with reciprocal monophyly, whereas sympatric populations of the species in Panama share identical or similar Mpi and Ci haplotypes, giving rise to genealogical polyphyly at the species level despite evidence for rapid sequence divergence at these genes between geographic races of H. melpomene. CONCLUSION: Recent transfer of Mpi haplotypes between species is strongly supported, but there is no evidence for introgression at the other three loci. Our results demonstrate that the boundaries between animal species can remain selectively porous to gene flow long after speciation, and that introgression, even between non-sibling species, can be an important factor in animal evolution. Interspecific gene flow is demonstrated here for the first time in Heliconius and may provide a route for the transfer of switch-gene adaptations for Müllerian mimicry. The results also forcefully demonstrate how reliance on a single locus may give an erroneous picture of the overall genealogical history of speciation and gene flow.

Animals↗

PubMed2003

Congenic mapping and candidate sequencing of susceptibility genes for Type 1 diabetes in the NOD mouse.

Inheritance of type 1 diabetes is polygenic with a major susceptibility gene located in the major histocompatibility complex (MHC). In addition to MHC-linked susceptibility, a number of susceptibility genes have been mapped outside the MHC in both humans and animal models. In order to localize and identify susceptibility genes for type 1 diabetes, we have developed a series of congenic strains in which either susceptibility intervals from the NOD mouse, a mouse model of type 1 diabetes, were introgressed onto control background genes or protective intervals from control strains were introgressed onto NOD background genes. NOD. CTS-H-2 congenic mice, which possess recombinant MHC with NOD alleles at class II A and E genes, which are candidates for Idd1, revealed that Idd1 consists of multiple components, one in class II (Idd1) and the other adjacent to, but distinct from, Idd1 (Idd16). Phenotypes of NOD. IIS-Idd3 congenic mice, which share the same alleles at both Il2 and Il21 as the NOD mouse, were indistinguishable from the NOD parental strain, indicating that both Il2 and Il21 are candidates for Idd3. In contrast, NOD. IIS-Idd10 congenic mice, which share the same alleles at Fcgr1, a previous candidate for Idd10, as the NOD mouse, were protected from type 1 diabetes, suggesting that Fcgr1 may not be responsible for the Idd10 effect. These data suggest that the use of strain colony closely related to a disease model to find the same candidate mutation on different haplotypes and make congenic strains with this recombinant chromosome, termed ancestral haplotype congenic mapping, is an effective strategy for fine mapping and identification of genes responsible for complex traits.

Animals↗

PubMed2006

Genetic interactions underlying hybrid male sterility in the Drosophila bipectinata species complex.

Understanding genetic mechanisms underlying hybrid male sterility is one of the most challenging problems in evolutionary biology especially speciation. By using the interspecific hybridization method roles of Y chromosome, Major Hybrid Sterility (MHS) genes and cytoplasm in sterility of hybrid males have been investigated in a promising group, the Drosophila bipectinata species complex that consists of four closely related species: D. pseudoananassae, D. bipectinata, D. parabipectinata and D. malerkotliana. The interspecific introgression analyses show that neither cytoplasm nor MHS genes are involved but X-Y interactions may be playing major role in hybrid male sterility between D. pseudoananassae and the other three species. The results of interspecific introgression analyses also show considerable decrease in the number of males in the backcross offspring and all males have atrophied testes. There is a significant positive correlation between sex - ratio distortion and severity of sterility in backcross males. These findings provide evidence that D. pseudoananassae is remotely related with other three species of the D. bipectinata species complex.

Animals↗

PubMed2004

Deletion of a disease resistance nucleotide-binding-site leucine-rich- repeat-like sequence is associated with the loss of the Phytophthora resistance gene Rps4 in soybean.

Resistance of soybean against the oomycete pathogen Phytophthora sojae is conferred by a series of Rps genes. We have characterized a disease resistance gene-like sequence NBSRps4/6 that was introgressed into soybean lines along with Rps4 or Rps6. High-resolution genetic mapping established that NBSRps4/6 cosegregates with Rps4. Two mutants, M1 and M2, showing rearrangements in the NBSRps4/6 region were identified from analyses of 82 F(1)'s and 201 selfed HARO4272 plants containing Rps4. Fingerprints of these mutants are identical to those of HARO4272 for 176 SSR markers representing the whole genome except the NBSRps4/6 region. Both mutants showed a gain of race specificities, distinct from the one encoded by Rps4. To investigate the possible mechanism of gain of Phytophthora resistance in M1, the novel race specificity was mapped. Surprisingly, the gene encoding this resistance mapped to the Rps3 region, indicating that this gene could be either allelic or linked to Rps3. Recombinant analyses have shown that deletion of NBSRps4/6 in M1 is associated with the loss of Rps4 function. The NBSRps4/6 sequence is highly transcribed in etiolated hypocotyls expressing the Phytophthora resistance. It is most likely that a copy of the NBSRps4/6 sequence is the Rps4 gene. Possible mechanisms of the deletion in the NBSRps4/6 region and introgression of two unlinked Rps genes into Harosoy are discussed.

Haplotypes↗

PubMed2005

Selection theory for marker-assisted backcrossing.

Marker-assisted backcrossing is routinely applied in breeding programs for gene introgression. While selection theory is the most important tool for the design of breeding programs for improvement of quantitative characters, no general selection theory is available for marker-assisted backcrossing. In this treatise, we develop a theory for marker-assisted selection for the proportion of the genome originating from the recurrent parent in a backcross program, carried out after preselection for the target gene(s). Our objectives were to (i) predict response to selection and (ii) give criteria for selecting the most promising backcross individuals for further backcrossing or selfing. Prediction of response to selection is based on the marker linkage map and the marker genotype of the parent(s) of the backcross population. In comparison to standard normal distribution selection theory, the main advantage of our approach is that it considers the reduction of the variance in the donor genome proportion due to selection. The developed selection criteria take into account the marker genotype of the candidates and consider whether these will be used for selfing or backcrossing. Prediction of response to selection is illustrated for model genomes of maize and sugar beet. Selection of promising individuals is illustrated with experimental data from sugar beet. The presented approach can assist geneticists and breeders in the efficient design of gene introgression programs.

Alleles↗

PubMed2005

Genetic mapping of species boundaries in Louisiana irises using IRRE retrotransposon display markers.

Genetic mapping studies provide insight into the pattern and extent of genetic incompatibilities affecting hybridization between closely related species. Genetic maps of two species of Louisiana Irises, Iris fulva and I. brevicaulis, were constructed from transposon-based molecular markers segregating in reciprocal backcross (BC1) interspecific hybrids and used to investigate genomic patterns of species barriers inhibiting introgression. Linkage mapping analyses indicated very little genetic incompatibility between I. fulva and I. brevicaulis in the form of map regions exhibiting transmission ratio distortion, and this was confirmed using a Bayesian multipoint mapping analysis. These results demonstrate the utility of transposon-based marker systems for genetic mapping studies of wild plant species and indicate that the genomes of I. fulva and I. brevicaulis are highly permeable to gene flow and introgression from one another via backcrossing.

Chromosome Mapping↗

PubMed2006

Evaluation of the genomic extent of effects of fixed inversion differences on intraspecific variation and interspecific gene flow in Drosophila pseudoobscura and D. persimilis.

There is increasing evidence that chromosomal inversions may facilitate the formation or persistence of new species by allowing genetic factors conferring species-specific adaptations or reproductive isolation to be inherited together and by reducing or eliminating introgression. However, the genomic domain of influence of the inverted regions on introgression has not been carefully studied. Here, we present a detailed study on the consequences that distance from inversion breakpoints has had on the inferred level of gene flow and divergence between Drosophila pseudoobscura and D. persimilis. We identified the locations of the inversion breakpoints distinguishing D. pseudoobscura and D. persimilis in chromosomes 2, XR, and XL. Population genetic data were collected at specific distances from the inversion breakpoints of the second chromosome and at two loci inside the XR and XL inverted regions. For loci outside the inverted regions, we found that distance from the nearest inversion breakpoint had a significant effect on several measures of divergence and gene flow between D. pseudoobscura and D. persimilis. The data fitted a logarithmic relationship, showing that the suppression of crossovers in inversion heterozygotes also extends to loci located outside the inversion but close to it (within 1-2 Mb). Further, we detected a significant reduction in nucleotide variation inside the inverted second chromosome region of D. persimilis and near one breakpoint, consistent with a scenario in which this inversion arose and was fixed in this species by natural selection.

Animals↗

PubMed2006

Development of a near-isogenic line population of Arabidopsis thaliana and comparison of mapping power with a recombinant inbred line population.

In Arabidopsis recombinant inbred line (RIL) populations are widely used for quantitative trait locus (QTL) analyses. However, mapping analyses with this type of population can be limited because of the masking effects of major QTL and epistatic interactions of multiple QTL. An alternative type of immortal experimental population commonly used in plant species are sets of introgression lines. Here we introduce the development of a genomewide coverage near-isogenic line (NIL) population of Arabidopsis thaliana, by introgressing genomic regions from the Cape Verde Islands (Cvi) accession into the Landsberg erecta (Ler) genetic background. We have empirically compared the QTL mapping power of this new population with an already existing RIL population derived from the same parents. For that, we analyzed and mapped QTL affecting six developmental traits with different heritability. Overall, in the NIL population smaller-effect QTL than in the RIL population could be detected although the localization resolution was lower. Furthermore, we estimated the effect of population size and of the number of replicates on the detection power of QTL affecting the developmental traits. In general, population size is more important than the number of replicates to increase the mapping power of RILs, whereas for NILs several replicates are absolutely required. These analyses are expected to facilitate experimental design for QTL mapping using these two common types of segregating populations.

Arabidopsis↗

PubMed2001

Low intraspecific variation for genomic isolation between hybridizing sunflower species.

Barriers to gene flow between species result from selection against foreign linkage blocks in hybrids. When the geographic ranges of taxa meet at multiple locations, the opportunity exists for variation in the genetic architecture of isolating barriers. Hybrid zones between two sunflower species (Helianthus annuus and H. petiolaris) in Nebraska and California exhibited remarkably similar patterns of introgression of mapped molecular markers. Congruence among hybrid zones may result from limited intraspecific variation at loci contributing to isolation and from similar selective effects of alleles in the heterospecific genetic background. The observed consistency of introgression patterns across distantly separated hybrid zones suggests that intrinsic forces predominate in determining hybrid zone dynamics and boundaries between these sunflower species.

Alleles↗

PubMed2003

Evolution of ascariasis in humans and pigs: a multi-disciplinary approach.

The nematode parasite Ascaris lumbricoides infects the digestive tracts of over 1.4 billion people worldwide, and its sister species, Ascaris suum, has infected a countless number of domesticated and feral pigs. It is generally thought that the putative ancestor to these worms infected either humans or pigs, but with the advent of domestication, they had ample opportunity to jump to a new host and subsequently specialize and evolve into a new species. While nuclear DNA makers decisively separate the two populations, mitochondrial sequences reveal that three major haplotypes are found in A. suum and in A. lumbricoides, indicating either occasional hybridization, causing introgression of gene trees, or retention of polymorphism dating back to the original ancestral species. This article provides an illustration of the combined contribution of parasitology, archaeoparasitology, genetics and paleogenetics to the history of ascariasis. We specifically investigate the molecular history of ascariasis in humans by sequencing DNA from the eggs of Ascaris found among ancient archeological remains. The findings of this paleogenetic survey will explain whether the three mitochondrial haplotypes result from recent hybridization and introgression, due to intensive human-pig interaction, or whether their co-occurrence predates pig husbandry, perhaps dating back to the common ancestor. We hope to show how human-pig interaction has shaped the recent evolutionary history of this disease, perhaps revealing the identify of the ancestral host.

Animals↗

PubMed1998

Genomic approaches to the improvement of disease resistance in farm animals.

As a result of the difficulties in improving disease resistance in farm animals by traditional phenotype selection, the achievement of such improvement is one of the most important applications of genome research. The major hurdle to this important goal is the collection of informative disease records to enable the segregation of disease resistance loci (DRL) to be traced in pedigrees. This paper reviews the principles for DRL identification by association analyses or by linkage analyses. Once linkage has been established, the location of the DRL may be further refined, a process which may eventually lead to the molecular characterisation of the causative gene(s) and mutation(s). A reliable map assignment of a DRL is sufficient for the practical utilisation of this knowledge, since the inheritance of the DRL can be traced by flanking markers. Marker-assisted selection concerns the use of linked markers for selection within populations, while marker-assisted introgression is used if DRL alleles are introgressed from a donor (resource) population.

Animals↗

PubMed2004

Notes on a discrepancy in mitochondrial DNA and allozyme differentiation in a pond frog Rana nigromaculata.

Analyses of complete 1143-base pair sequence of the mitochondrial cytochrome b gene demonstrated a sister relationship between Japanese R. nigromaculata and Korean R. plancyichosenica, but not with Korean R. nigromaculata, while the allozyme data strongly supported the monophyly of the Korean and Japanese populations of R. nigromaculata. We surmise this discordance to be the result of the inheritance of introduced mtDNA and the dilution of introduced nuclear DNA in mixed lineages after past hybridization and genome introgression between the two species, although the direction of introgression is unknown.

Animals↗

PubMed2003

Intra- and interspecific genetic complexities of two Eothenomys species in Honshu, Japan.

Differences in the nuclear ribosomal DNA (rDNA), mitochondrial DNA (mtDNA), cytochrome b (Cytb), and Y chromosomal Sry genes were used to assess intra- and interspecific relationships in two Japanese red-backed voles, Eothenomys andersoni and E. smithii, focusing on areas where the two species might come into contact. In the Kii Peninsula, southwestern Honshu, which contains an allopatric population of E. andersoni isolated from its main range, the rDNA-RFLP data provide robust evidence of past mutual interspecific gene introgression, while the Cytb and Sry sequences were specific to this population. In central Honshu, where E. andersoni and E. smithii inhabit higher and lower altitudes, respectively, with a narrow sympatric zone, the rDNA-RFLP and Sry variation was specific for each species, while introgression of the mtDNA from E. smithii to E. andersoni was seen. These complex patterns in the gene markers are consistent with our previous notions derived from sex chromosome variation. Our previous and present data strongly suggest that the evolution of these vole species, which are morphologically and cytogenetically distinct, involves complex genetic interactions and the resultant combinations of genes are sometimes peculiar, mainly due to the Cytb haplotypes. However, phylogenetic analysis using a combination of maternal, paternal, and biparental markers has proven useful for understanding the evolutionary history given the complex phylogenetic background.

Animals↗

PubMed2006

The current status and environmental impacts of glyphosate-resistant crops: a review.

Glyphosate [N-(phosphonomethyl) glycine]-resistant crops (GRCs), canola (Brassica napus L.), cotton (Gossypium hirsutum L.), maize (Zea mays L.), and soybean [Glycine max (L.) Merr.] have been commercialized and grown extensively in the Western Hemisphere and, to a lesser extent, elsewhere. Glyphosate-resistant cotton and soybean have become dominant in those countries where their planting is permitted. Effects of glyphosate on contamination of soil, water, and air are minimal, compared to some of the herbicides that they replace. No risks have been found with food or feed safety or nutritional value in products from currently available GRCs. Glyphosate-resistant crops have promoted the adoption of reduced- or no-tillage agriculture in the USA and Argentina, providing a substantial environmental benefit. Weed species in GRC fields have shifted to those that can more successfully withstand glyphosate and to those that avoid the time of its application. Three weed species have evolved resistance to glyphosate in GRCs. Glyphosate-resistant crops have greater potential to become problems as volunteer crops than do conventional crops. Glyphosate resistance transgenes have been found in fields of canola that are supposed to be non-transgenic. Under some circumstances, the largest risk of GRCs may be transgene flow (introgression) from GRCs to related species that might become problems in natural ecosystems. Glyphosate resistance transgenes themselves are highly unlikely to be a risk in wild plant populations, but when linked to transgenes that may impart fitness benefits outside of agriculture (e.g., insect resistance), natural ecosystems could be affected. The development and use of failsafe introgression barriers in crops with such linked genes is needed.

Argentina↗

PubMed2005

Ultrafine mapping of SNPs from mouse strains C57BL/6J, DBA/2J, and C57BLKS/J for loci contributing to diabetes and atherosclerosis susceptibility.

The inbred mouse strain C57BLKS/J (BKS) carrying a mutation of the leptin receptor lepr(-/-) (BKS-db) is a classic mouse model of type 2 diabetes. While BKS was originally presumed to be a substrain of C57BL/6J (B6), it has become apparent that its genome contains introgressed regions from a DBA/2 (DBA)-like strain and perhaps other unidentified sources. It has been hypothesized that the strikingly enhanced diabetes susceptibility of BKS-db compared with B6-db is conferred by this introgressed DNA. Using high-density single nucleotide polymorphisms, we have mapped the DBA and other contaminating DNA regions present in BKS. Thus, approximately 70% of its genome appears to derive from B6, with approximately 20% from DBA and another 9% from an unidentified donor. Comparison with 56 diverse inbred strains suggests that this donor may be a less common inbred strain or an outbred or wild strain. Using expression data from a B6 x DBA cross, we identified differentially regulated genes between these two strains. Those cis-regulated genes located on DBA-like blocks in BKS constitute primary candidates for genes contributing to diabetes susceptibility in the BKS-db strain. To further prioritize these candidates, we identified those cis-acting expression quantitative trait loci whose expression significantly correlates with diabetes-related phenotypes.

Animals↗

PubMed1993

Challenges and opportunities for integrating genetically modified animals into traditional animal breeding plans.

Techniques have been developed to introduce specific genes from one species into the germplasm of another, including livestock. This paper reviews reports on evaluation, selection, and breeding procedures for introduction and multiplication of transgenes in breeding populations of livestock. Before transgenes are introduced and multiplied in commercial breeding populations, it is necessary to test transgenics extensively for both favorable and unfavorable transgene effects. Parent stock used to produce transgenic founder animals should be selected to excel in polygenic breeding value for economically important traits, especially if founder animals or their sons are to be used directly by AI in commercial populations. However, polygenic breeding value of founder transgenic animals and inbreeding depression are of negligible importance if a transgene is introgressed into a selection nucleus population from three or four generations of backcrossing. Transgenic development should be economically viable for traits with major effects on net merit, especially in the dairy industry, where transgenic sires can be used extensively by AI. A minimum effect of about 10% of the mean (or one phenotypic standard deviation) is a reasonable approximation of the minimum transgene effect that would be necessary to justify introgression into a nucleus swine population. A transgene effect of 10 to 20% of the mean would be required for most economic traits in beef cattle.

Animals↗

PubMed2025

Whole Genome Development of Specific Alien-Chromosome Oligo (SAO) Markers for Wild Peanut Chromosomes Based on Chorus2.

The cultivated peanut (Arachis hypogaea L.) is a globally important oilseed and economic crop, but its narrow genetic base limits breeding progress. Wild Arachis species represent valuable genetic resources for enhancing the resilience of the peanut cultigen. While wild species from section Arachis are widely used in breeding programs, the detection of alien chromosomes in hybrids remains challenging due to limited molecular tools. In this study, a cost-effective and efficient system was established for generating species-specific molecular markers using low-coverage next-generation sequencing data, bypassing the need for whole-genome assembly. Utilizing the Chorus2 software, specific alien-chromosome oligo (SAO) markers were developed for four wild species, A. duranensis (accession A19), A. pusilla (A10), A. appresipilla (A33), and A. glabrata (G2 and G3). A total of 1166 primer pairs were designed, resulting in 220 SAO markers specific to A. duranensis, 77 to A. pusilla, 112 to A. appresipilla, 69 to A. glabrata G2, and 59 to A. glabrata G3, with the highest development efficiency observed in A. duranensis (55.0%). These markers span all chromosomes of the five wild accessions. Genome-wide, chromosome-specific SAO markers enable the efficient detection of introgressed alien chromosomes and provide insight into syntenic relationships among homoeologous chromosomes. These markers offer an effective tool for identifying favorable genes and facilitating targeted introgression for the genetic improvement of the cultivated peanut.

Chorus2↗

PubMed2026

Evaluating three alternative scenarios for the origin of a disjunct Arctium tomentosum population in the Pyrenees.

BACKGROUND: Disjunctions in species distributions offer natural experiments for investigating the mechanisms underlying distributional breaks, such as range contraction, long-distance pollen transport, or long-distance seed dispersal. Here, we document and characterise a floristic novelty in the Pyrenean and Iberian regions, and use it as a case study to investigate the processes underlying disjunct species distributions. Our analysis focuses on Arctium L. (burdocks), a genus native to Eurasia comprising several cosmopolitan weedy species. It is characterised by hooked capitula that facilitate epizoochorous dispersal. METHODS: To clarify the taxonomic identity of a previously undocumented Pyrenean population resembling A. tomentosum, we adopted an integrative approach, combining distribution information, morphology, genome size, repetitive DNA analysis and chloroplast data across the four known European species. Additionally, we conducted a comparative study of functional capitulum traits, predispersal fruit predation, and associated entomofauna for the newly discovered population and nearby A. minus populations. RESULTS: The discovered population constitutes a floristic novelty for the region and is identified as A. tomentosum, exhibiting signatures of past introgression from A. minus, as indicated by cytonuclear discordance. We evaluated three alternative scenarios to explain its origin: (i) persistence as a relict from a previously wider distribution, (ii) long-distance pollination by migrating insects, and (iii) long-distance seed dispersal from an A. tomentosum population with a history of past introgression. Of these, only the third is consistent with the available evidence. These results highlight the complexity of interpreting disjunct species distributions and underscore the value of integrative approaches for resolving population identity, origin, dispersal, and persistence across environments.

Arctium↗